They were attempting to cross the Rainbow Bridge on March 16, according to a news release issued Monday by Toronto police.
Border officers had been acting on information provided to them by the firearm enforcement unit, police said.
Along with the handguns, border officers said they also found knives, ammunition and "two inert hand grenades" inside the van. Officers also found an additional handgun, which was allegedly located "on the man."
Police said they subsequently searched the couple’s home and found an additional 34 guns.
A 44-year-old man and a 43-year-old woman from Proton Station, Ont., face dozens of firearm related charges.
The accused are due to appear in a Toronto court on Tuesday morning.